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Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor2015-03-03BiotechnologyPlant ScienceSaccharification of polysaccharides releases monosaccharides that can be used by ethanol-producing microorganisms in biofuel production. To improve plant biomass as a raw material for saccharification, factors controlling the accumulation and structure of carbohydrates must be identified. Rice SUB1A-1 is a transcription factor that represses the turnover of starch and postpones energy-consuming growth processes under submergence stress. Arabidopsis was employed to test if heterologous expression of SUB1A-1 or SUB1C-1 (a related gene) can be used to improve saccharification. Cellulolytic and amylolytic enzymatic treatments confirmed that SUB1A-1 transgenics had better saccharification yield than wild-type (Col-0), mainly from accumulated starch. This improved saccharification yield was developmentally controlled; when compared to Col-0, young transgenic vegetative plants yielded 200–300% more glucose, adult vegetative plants yielded 40–90% more glucose and plants in reproductive stage had no difference in yield. We measured photosynthetic parameters, starch granule microstructure, and transcript abundance of genes involved in starch degradation (SEX4, GWD1), juvenile transition (SPL3-5) and meristematic identity (FUL, SOC1) but found no differences to Col-0, indicating that starch accumulation may be controlled by down-regulation of CONSTANS and FLOWERING LOCUS T by SUB1A-1 as previously reported. SUB1A-1 transgenics also offered less resistance to deformation than wild-type concomitant to up-regulation of AtEXP2 expansin and BGL2 glucan-1,3,-beta-glucosidase. We conclude that heterologous SUB1A-1 expression can improve saccharification yield and softness, two traits needed in bioethanol production.https://peerj.com/articles/816
The use of neuralgia medications to treat sensory neuropathic cough: our experience in a retrospective cohort of thirty-two patients2015-03-03Clinical TrialsNeurologyOtorhinolaryngologyObjective. This study sought to: (1) quantify response rate and efficacy of amitriptyline, desipramine, and gabapentin in treating sensory neuropathic cough; and (2) describe an efficient treatment protocol.Study Design. This study is a retrospective case series.Methods. Persons diagnosed with sensory neuropathic cough during a one-year period were potential study candidates. To bolster the diagnosis credibility, only persons who had been treated elsewhere for gastroesophageal reflux disease, asthma, and allergy with no reduction of cough were included. Upon diagnosis of sensory neuropathic cough, each person was treated with either amitriptyline, desipramine, or gabapentin, titrating the dose upward to desired benefit or the dose limit. If the benefit was insufficient, another of the medications was used next, using a similar dose escalation strategy. Data points included patient demographics, initial and final medication, final dose, and degree of improvement.Results. 32 patients met the diagnostic and inclusion criteria and had a complete data set. 94% (30 of 32) of the patients responded to at least one of the medications. The 32 patients undertook a total of 45 single-medication trials. Patients reported symptom relief during 78% (14 of 18) of amitriptyline trials, 73% (11 of 15) of desipramine trials, and 83% (10 of 12) of gabapentin trials. At final dosage, symptom reduction averaged 77% on amitriptyline, 73% on desipramine, and 69% on gabapentin.Conclusion. Amitriptyline, desipramine, and gabapentin appear to vary in their effectiveness for individual cases of sensory neuropathic cough; across a whole cohort, symptom relief was similar in frequency and degree on any of the three medications. More evidence is needed to demonstrate more convincingly the effectiveness of these medications, but this data set suggests that each of these three medications deserves consideration in the codified treatment protocol presented here.https://peerj.com/articles/814
Pallid bands in feathers and associated stable isotope signatures reveal effects of severe weather stressors on fledgling sparrows2015-03-03Conservation BiologyEcologyZoologyIn August 2013, we observed a high incidence (44%) of synchronous bands of reduced melanin (a type of fault bar we have termed “pallid bands”) across the rectrices of juvenile Grasshopper Sparrows (Ammodrammus savannarum) captured near El Reno, Oklahoma. Earlier that year, on May 31, the site was struck by a severe storm which rained hailstones exceeding 5.5 cm diameter and spawned an historic 4.2 km-wide tornado <8 km to the south of the site. We hypothesized that this stressor had induced the pallid bands. An assessment of Grasshopper Sparrow nesting phenology indicated that a large number of nestlings were likely growing tail feathers when the storm hit. The pallid bands were restricted to the distal half of feathers and their widths significantly increased as a function of distance from the tip (i.e., age at formation). We predicted that if stress had caused these pallid bands, then a spike in circulating δ15N originating from tissue catabolism during the stress response would have been incorporated into the developing feather. From 18 juveniles captured at the site in August we measured δ15N and δ13C stable isotope ratios within four to five 0.25–0.40 mg feather sections taken from the distal end of a tail feather; the pallid band, if present, was contained within only one section. After accounting for individual and across-section variation, we found support for our prediction that feather sections containing or located immediately proximal to pallid bands (i.e., the pallid band region) would show significantly higher δ15N than sections outside this region. In contrast, the feathers of juveniles with pallid bands compared to normal appearing juveniles showed significantly lower δ15N. A likely explanation is that the latter individuals hatched after the May 31 storm and had consumed a trophically-shifted diet relative to juveniles with pallid bands. Considering this, the juveniles of normal appearance were significantly less abundant within our sample relative to expectations from past cohorts (z = − 2.03; p = 0.042) and, in as much, suggested widespread nest losses during the storm. Severe weather events may represent major stressors to ground-nesting birds, especially for recent fledglings. We call for others to exploit opportunities to study the effects of severe weather when these rare but devastating stressors impact established field research sites.https://peerj.com/articles/812
Rapid morphological change in black rats (Rattus rattus) after an island introduction2015-03-03BiodiversityConservation BiologyEcologyEvolutionary StudiesZoologyRapid morphological change has been shown in rodent populations on islands, including endemic deer mice (Peromyscus maniculatus subspp.) on the California Channel Islands. Surprisingly, most of these changes were towards a smaller size. Black rats were introduced to Anacapa Island in the mid-1800s (probably in 1853) and eradicated in 2001–2002. To assess possible changes in these rats since their introduction, eleven cranial and four standard external measurements were taken from 59 Rattus rattus specimens collected from 1940–2000. All rat cranial traits changed 3.06–10.43% (724–2567 d, 0.06–0.42 h), and all became larger. When considered in haldanes, these changes are among the fastest on record in any organism, and far exceed changes found in other island rodents. These changes were confirmed by MANOVA (Wilk’s λ < 0.0005, Fd.f.15 = 2974.386, P < 0.0005), and all 11 cranial traits significantly fit linear regressions. We speculate that concurrent changes in mice may have been due in part to competition with and/or predation by rats. Future research might evaluate whether the vector of mouse evolution on Anacapa is again changing after rat eradication.https://peerj.com/articles/808
Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space2015-03-03BioinformaticsGenomicsComputational ScienceWhen computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.https://peerj.com/articles/803
Development modeling of Lucilia sericata (Diptera: Calliphoridae)2015-03-03Developmental BiologyEntomologyThe relationship between insect development and temperature has been well established and has a wide range of uses, including the use of blow flies for postmortem (PMI) interval estimations in death investigations. To use insects in estimating PMI, we must be able to determine the insect age at the time of discovery and backtrack to time of oviposition. Unfortunately, existing development models of forensically important insects are only linear approximations and do not take into account the curvilinear properties experienced at extreme temperatures. A series of experiments were conducted with Lucilia sericata, a forensically important blow fly species, that met the requirements needed to create statistically valid development models. Experiments were conducted over 11 temperatures (7.5 to 32.5 °C, at 2.5 °C) with a 16:8 L:D cycle. Experimental units contained 20 eggs, 10 g beef liver, and 2.5 cm of pine shavings. Each life stage (egg to adult) had five sampling times. Each sampling time was replicated four times, for a total of 20 measurements per life stage. For each sampling time, the cups were pulled from the chambers and the stage of each maggot was documented morphologically through posterior spiracle slits and cephalopharyngeal skeletal development. Data were normally distributed with the later larval stages (L3f, L3m) having the most variation within and transitioning between stages. The biological minimum was between 7.5 °C and 10 °C, with little egg development and no egg emergence at 7.5 °C. Temperature-induced mortality was highest from 10.0 to 17.5 °C and 32.5 °C. The development data generated illustrates the advantages of large datasets in modeling Lucilia sericata development and the need for curvilinear models in describing development at environmental temperatures near the biological minima and maxima.https://peerj.com/articles/796
VaRank: a simple and powerful tool for ranking genetic variants2015-03-03BioinformaticsGeneticsGenomicsBackground. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians.Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients.Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/.https://peerj.com/articles/794
Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files2015-03-03BioinformaticsRadiology and Medical ImagingTranslational MedicineScience and Medical EducationComputational ScienceThe Portable Document Format (PDF) allows for embedding three-dimensional (3D) models and is therefore particularly suitable to communicate respective data, especially as regards scholarly articles. The generation of the necessary model data, however, is still challenging, especially for inexperienced users. This prevents an unrestrained proliferation of 3D PDF usage in scholarly communication. This article introduces a new solution for the creation of three of types of 3D geometry (point clouds, polylines and triangle meshes), that is based on MeVisLab, a framework for biomedical image processing. This solution enables even novice users to generate the model data files without requiring programming skills and without the need for an intensive training by simply using it as a conversion tool. Advanced users can benefit from the full capability of MeVisLab to generate and export the model data as part of an overall processing chain. Although MeVisLab is primarily designed for handling biomedical image data, the new module is not restricted to this domain. It can be used for all scientific disciplines.https://peerj.com/articles/789
Evolution of resistance and tolerance to herbivores: testing the trade-off hypothesis2015-03-03EcologyEvolutionary StudiesGeneticsBackground. To cope with their natural enemies, plants rely on resistance and tolerance as defensive strategies. Evolution of these strategies among natural population can be constrained by the absence of genetic variation or because of the antagonistic genetic correlation (trade-off) between them. Also, since plant defenses are integrated by several traits, it has been suggested that trade-offs might occur between specific defense traits.Methodology/Principal Findings. We experimentally assessed (1) the presence of genetic variance in tolerance, total resistance, and leaf trichome density as specific defense trait, (2) the extent of natural selection acting on plant defenses, and (3) the relationship between total resistance and leaf trichome density with tolerance to herbivory in the annual herb Datura stramonium. Full-sib families of D. stramonium were either exposed to natural herbivores (control) or protected from them by a systemic insecticide. We detected genetic variance for leaf trichome density, and directional selection acting on this character. However, we did not detect a negative significant correlation between tolerance and total resistance, or between tolerance and leaf trichome density. We argue that low levels of leaf damage by herbivores precluded the detection of a negative genetic correlation between plant defense strategies.Conclusions/Significance. This study provides empirical evidence of the independent evolution of plant defense strategies, and a defensive role of leaf trichomes. The pattern of selection should favor individuals with high trichomes density. Also, because leaf trichome density reduces damage by herbivores and possess genetic variance in the studied population, its evolution is not constrained.https://peerj.com/articles/785
Body composition in Nepalese children using isotope dilution: the production of ethnic-specific calibration equations and an exploration of methodological issues2015-03-03Anatomy and PhysiologyDiabetes and EndocrinologyEpidemiologyGlobal HealthNutritionBackground. Body composition is important as a marker of both current and future health. Bioelectrical impedance (BIA) is a simple and accurate method for estimating body composition, but requires population-specific calibration equations.Objectives. (1) To generate population specific calibration equations to predict lean mass (LM) from BIA in Nepalese children aged 7–9 years. (2) To explore methodological changes that may extend the range and improve accuracy.Methods. BIA measurements were obtained from 102 Nepalese children (52 girls) using the Tanita BC-418. Isotope dilution with deuterium oxide was used to measure total body water and to estimate LM. Prediction equations for estimating LM from BIA data were developed using linear regression, and estimates were compared with those obtained from the Tanita system. We assessed the effects of flexing the arms of children to extend the range of coverage towards lower weights. We also estimated potential error if the number of children included in the study was reduced.Findings. Prediction equations were generated, incorporating height, impedance index, weight and sex as predictors (R2 93%). The Tanita system tended to under-estimate LM, with a mean error of 2.2%, but extending up to 25.8%. Flexing the arms to 90° increased the lower weight range, but produced a small error that was not significant when applied to children <16 kg (p 0.42). Reducing the number of children increased the error at the tails of the weight distribution.Conclusions. Population-specific isotope calibration of BIA for Nepalese children has high accuracy. Arm position is important and can be used to extend the range of low weight covered. Smaller samples reduce resource requirements, but leads to large errors at the tails of the weight distribution.